Jiyan He

Yu Shi, Shuxin Zheng, Guolin Ke et al. · microsoft-research, tsinghua

This technical note describes the recent updates of Graphormer, including architecture design modifications, and the adaption to 3D molecular dynamics simulation. With these simple modifications, Graphormer could attain better results on large-scale molecular modeling datasets than the vanilla one, and the performance gain could be consistently obtained on 2D and 3D molecular graph modeling tasks. In addition, we show that with a global receptive field and an adaptive aggregation strategy, Graphormer is more powerful than classic message-passing-based GNNs. Empirically, Graphormer could achieve much less MAE than the originally reported results on the PCQM4M quantum chemistry dataset used in KDD Cup 2021. In the meanwhile, it greatly outperforms the competitors in the recent Open Catalyst Challenge, which is a competition track on NeurIPS 2021 workshop, and aims to model the catalyst-adsorbate reaction system with advanced AI models. All codes could be found at https://github.com/Microsoft/Graphormer.

Jiyan He, Xuechen Li, Da Yu et al. · microsoft-research, stanford

Differentially private deep learning has recently witnessed advances in computational efficiency and privacy-utility trade-off. We explore whether further improvements along the two axes are possible and provide affirmative answers leveraging two instantiations of \emph{group-wise clipping}. To reduce the compute time overhead of private learning, we show that \emph{per-layer clipping}, where the gradient of each neural network layer is clipped separately, allows clipping to be performed in conjunction with backpropagation in differentially private optimization. This results in private learning that is as memory-efficient and almost as fast per training update as non-private learning for many workflows of interest. While per-layer clipping with constant thresholds tends to underperform standard flat clipping, per-layer clipping with adaptive thresholds matches or outperforms flat clipping under given training epoch constraints, hence attaining similar or better task performance within less wall time. To explore the limits of scaling (pretrained) models in differentially private deep learning, we privately fine-tune the 175 billion-parameter GPT-3. We bypass scaling challenges associated with clipping gradients that are distributed across multiple devices with \emph{per-device clipping} that clips the gradient of each model piece separately on its host device. Privately fine-tuning GPT-3 with per-device clipping achieves a task performance at $ε=1$ better than what is attainable by non-privately fine-tuning the largest GPT-2 on a summarization task.

Shuxin Zheng, Jiyan He, Chang Liu et al. · microsoft-research

Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather determined from the equilibrium distribution of structures. Traditional methods for obtaining these distributions, such as molecular dynamics simulation, are computationally expensive and often intractable. In this paper, we introduce a novel deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems. Inspired by the annealing process in thermodynamics, DiG employs deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system, such as a chemical graph or a protein sequence. This framework enables efficient generation of diverse conformations and provides estimations of state densities. We demonstrate the performance of DiG on several molecular tasks, including protein conformation sampling, ligand structure sampling, catalyst-adsorbate sampling, and property-guided structure generation. DiG presents a significant advancement in methodology for statistically understanding molecular systems, opening up new research opportunities in molecular science.

Zhenzhen Ren, Xinpeng Zhang, Zhenxing Qian et al. · microsoft-research

The integration of external tools is pivotal for empowering Large Language Model (LLM) agents with real-world capabilities. However, training these agents through direct, continuous interaction with diverse tools is often prohibitively expensive, slow, and introduces additional development and maintenance overhead. To address this challenge, we introduce the Generalist Tool Model (GTM), a 1.5-billion-parameter model that learns to act as a universal tool simulator. With only prompt-level configuration, GTM accesses tool functionalities along with input arguments and generates outputs that faithfully mimic real tool execution, providing a fast and cost-effective solution that eliminates development overhead. To build GTM, we propose the Context-Aware Response Generation (CARG) pipeline, which synthesizes comprehensive training data covering over 20,000 tools across 300 domains including physics, medicine, robotics, and finance. Through this pipeline, GTM learns to produce not only syntactically correct outputs but also logically coherent and contextually appropriate responses. Experiments demonstrate that GTM produces high-quality outputs with strong consistency and reliability. Besides when used in real reinforcement learning scenarios for agent training, GTM exhibits significantly faster simulation speed compared to real tools while maintaining comparable output quality, along with remarkable generalization and domain adaptability. Our results establish GTM as a foundational component for developing future AI agents, enabling efficient and scalable training of tool-augmented systems.

Zhaoxi Zhang, Yitong Duan, Yanzhi Zhang et al. · baidu, tsinghua

Locating files and functions requiring modification in large software repositories is challenging due to their scale and structural complexity. Existing LLM-based methods typically treat this as a repository-level retrieval task and rely on multiple auxiliary tools, which often overlook code execution logic and complicate model control. We propose RepoNavigator, an LLM agent equipped with a single execution-aware tool: jumping to the definition of an invoked symbol. This unified design reflects the actual flow of code execution while simplifying tool manipulation. RepoNavigator is trained end-to-end via Reinforcement Learning (RL) directly from a base pretrained model, without relying on closed-source distillation. Experiments demonstrate that RL-trained RepoNavigator achieves state-of-the-art performance, with the 7B model outperforming 14B baselines, the 14B model surpassing 32B competitors, and the 32B model exceeding closed-source models such as GPT-5 on most metrics. These results confirm that integrating a single, structurally grounded tool with RL training provides an efficient and scalable solution for repository-level issue localization.

Zhixin Han, Yanzhi Zhang, Chuyang Wei et al.

Live future prediction refers to the task of making predictions about real-world events before they unfold. This task is increasingly studied using large language model-based agent systems, and it is important for building agents that can continually learn from real-world. Just as interactive environments have often driven progress in agents, advancing live future prediction naturally motivates viewing it as a learning environment. Prior works have explored future prediction from several different parts, but have generally not framed it as a unified learning environment. This task is appealing for learning because it can provide a large number of prediction questions grounded in diverse real-world events, while preventing answer leakage. To leverage the advantages of live future prediction, we present FutureWorld, a live agentic reinforcement learning environment that closes the training loop between prediction, outcome realization, and parameters update. In our environment, we take three open-source base models and train them for consecutive days. The results show that training is effective. Furthermore, we build a daily benchmark based on the environment and evaluate several frontier agents on it to establish performance baselines for current agent systems.

Chuyang Wei, Maohang Gao, Zhixin Han et al.

Many consequential decisions must be made before the relevant outcome is known. Such problems are commonly framed as future prediction, where an LLM agent must form a prediction for an unresolved question using only the public information available at the prediction time. The setting is difficult because public evidence evolves while useful supervision arrives only after the question is resolved, so most existing approaches still improve mainly from final outcomes. Yet final outcomes are too coarse to guide earlier factor tracking, evidence gathering and interpretation, or uncertainty handling. When the same unresolved question is revisited over time, temporal contrasts between earlier and later predictions can expose omissions in the earlier prediction process; we call this signal internal feedback. We introduce Milkyway, a self-evolving agent system that keeps the base model fixed and instead updates a persistent future prediction harness for factor tracking, evidence gathering and interpretation, and uncertainty handling. Across repeated predictions on the same unresolved question, Milkyway extracts internal feedback and writes reusable guidance back into the harness, so later predictions on that question can improve before the outcome is known. After the question is resolved, the final outcome provides a retrospective check before the updated harness is carried forward to subsequent questions. On FutureX and FutureWorld, Milkyway achieves the best overall score among the compared methods, improving FutureX from 44.07 to 60.90 and FutureWorld from 62.22 to 77.96.

Yanxi Wang, Zhiling Zhang, Wenbo Zhou et al.

GUI agents enable end-to-end automation through direct perception of and interaction with on-screen interfaces. However, these agents frequently access interfaces containing sensitive personal information, and screenshots are often transmitted to remote models, creating substantial privacy risks. These risks are particularly severe in GUI workflows: GUIs expose richer, more accessible private information, and privacy risks depend on interaction trajectories across sequential scenes. We propose GUIGuard, a three-stage framework for privacy-preserving GUI agents: (1) privacy recognition, (2) privacy protection, and (3) task execution under protection. We further construct GUIGuard-Bench, a cross-platform benchmark with 630 trajectories and 13,830 screenshots, annotated with region-level privacy grounding and fine-grained labels of risk level, privacy category, and task necessity. Evaluations reveal that existing agents exhibit limited privacy recognition, with state-of-the-art models achieving only 13.3% accuracy on Android and 1.4% on PC. Under privacy protection, task-planning semantics can still be maintained, with closed-source models showing stronger semantic consistency than open-source ones. Case studies on MobileWorld show that carefully designed protection strategies achieve higher task accuracy while preserving privacy. Our results highlight privacy recognition as a critical bottleneck for practical GUI agents. Project: https://futuresis.github.io/GUIGuard-page/

Yu Shi, Shuxin Zheng, Guolin Ke et al.

This technical note describes the recent updates of Graphormer, including architecture design modifications, and the adaption to 3D molecular dynamics simulation. The "Graphormer-V2" could attain better results on large-scale molecular modeling datasets than the vanilla one, and the performance gain could be consistently obtained on downstream tasks. In addition, we show that with a global receptive field and an adaptive aggregation strategy, Graphormer is more powerful than classic message-passing-based GNNs. Graphormer-V2 achieves much less MAE than the vanilla Graphormer on the PCQM4M quantum chemistry dataset used in KDD Cup 2021, where the latter one won the first place in this competition. In the meanwhile, Graphormer-V2 greatly outperforms the competitors in the recent Open Catalyst Challenge, which is a competition track on NeurIPS 2021 workshop, and aims to model the catalyst-adsorbate reaction system with advanced AI models. All models could be found at \url{https://github.com/Microsoft/Graphormer}.

Yanzhi Zhang, Yitong Duan, Zhaoxi Zhang et al.

Test-time scaling has emerged as a promising direction for enhancing the reasoning capabilities of Large Language Models in last few years. In this work, we propose Population-Evolve, a training-free method inspired by Genetic Algorithms to optimize LLM reasoning. Our approach maintains a dynamic population of candidate solutions for each problem via parallel reasoning. By incorporating an evolve prompt, the LLM self-evolves its population in all iterations. Upon convergence, the final answer is derived via majority voting. Furthermore, we establish a unification framework that interprets existing test-time scaling strategies through the lens of genetic algorithms. Empirical results demonstrate that Population-Evolve achieves superior accuracy with low performance variance and computational efficiency. Our findings highlight the potential of evolutionary strategies to unlock the reasoning power of LLMs during inference.

Jiyan He, Weitao Feng, Yaosen Min et al. · microsoft-research

The expanding application of Artificial Intelligence (AI) in scientific fields presents unprecedented opportunities for discovery and innovation. However, this growth is not without risks. AI models in science, if misused, can amplify risks like creation of harmful substances, or circumvention of established regulations. In this study, we aim to raise awareness of the dangers of AI misuse in science, and call for responsible AI development and use in this domain. We first itemize the risks posed by AI in scientific contexts, then demonstrate the risks by highlighting real-world examples of misuse in chemical science. These instances underscore the need for effective risk management strategies. In response, we propose a system called SciGuard to control misuse risks for AI models in science. We also propose a red-teaming benchmark SciMT-Safety to assess the safety of different systems. Our proposed SciGuard shows the least harmful impact in the assessment without compromising performance in benign tests. Finally, we highlight the need for a multidisciplinary and collaborative effort to ensure the safe and ethical use of AI models in science. We hope that our study can spark productive discussions on using AI ethically in science among researchers, practitioners, policymakers, and the public, to maximize benefits and minimize the risks of misuse.

Yanzhi Zhang, Zhaoxi Zhang, Haoxiang Guan et al.

Reinforcement learning has emerged as a powerful paradigm for post-training large language models (LLMs) to improve reasoning. Approaches like Reinforcement Learning from Human Feedback (RLHF) and Reinforcement Learning with Verifiable Rewards (RLVR) have shown strong results, but they require extensive external supervision. We investigate an alternative class of methods, Reinforcement Learning from Internal Feedback (RLIF), which relies solely on intrinsic model-derived signals instead of external rewards. In particular, we leverage unsupervised reward proxies such as token-level entropy, trajectory-level entropy, and self-certainty. Our theoretical analysis shows these internal objectives are partially equivalent, and we empirically evaluate various RLIF strategies on challenging math reasoning benchmarks. Experimental results demonstrate that RLIF can boost the reasoning performance of base LLMs at the beginning phase of the training, matching or surpassing RLVR techniques on these tasks. However, when training progresses, performance degrades even below the model before training. Moreover, we find that RLIF yields little improvement for instruction-tuned models, indicating diminishing returns of intrinsic feedback once an LLM is already instruction-tuned. We further analyze this limitation by mixing model weights and explain the reason of RLIF's training behaviors, providing practical guidelines for integrating internal feedback signals into LLM training. We hope our analysis of internal feedback will inform more principled and effective strategies for LLM post-training.

Chenyu Li, Zhengjia Zhu, Jiyan He et al.

Internal threat detection (IDT) aims to address security threats within organizations or enterprises by identifying potential or already occurring malicious threats within vast amounts of logs. Although organizations or enterprises have dedicated personnel responsible for reviewing these logs, it is impossible to manually examine all logs entirely.In response to the vast number of logs, we propose a system called RedChronos, which is a Large Language Model-Based Log Analysis System. This system incorporates innovative improvements over previous research by employing Query-Aware Weighted Voting and a Semantic Expansion-based Genetic Algorithm with LLM-driven Mutations. On the public datasets CERT 4.2 and 5.2, RedChronos outperforms or matches existing approaches in terms of accuracy, precision, and detection rate. Moreover, RedChronos reduces the need for manual intervention in security log reviews by approximately 90% in the Xiaohongshu Security Operation Center. Therefore, our RedChronos system demonstrates exceptional performance in handling IDT tasks, providing innovative solutions for these challenges. We believe that future research can continue to enhance the system's performance in IDT tasks while also reducing the response time to internal risk events.

Yuxuan Ren, Dihan Zheng, Chang Liu et al. · microsoft-research

In recent years, machine learning has demonstrated impressive capability in handling molecular science tasks. To support various molecular properties at scale, machine learning models are trained in the multi-task learning paradigm. Nevertheless, data of different molecular properties are often not aligned: some quantities, e.g. equilibrium structure, demand more cost to compute than others, e.g. energy, so their data are often generated by cheaper computational methods at the cost of lower accuracy, which cannot be directly overcome through multi-task learning. Moreover, it is not straightforward to leverage abundant data of other tasks to benefit a particular task. To handle such data heterogeneity challenges, we exploit the specialty of molecular tasks that there are physical laws connecting them, and design consistency training approaches that allow different tasks to exchange information directly so as to improve one another. Particularly, we demonstrate that the more accurate energy data can improve the accuracy of structure prediction. We also find that consistency training can directly leverage force and off-equilibrium structure data to improve structure prediction, demonstrating a broad capability for integrating heterogeneous data.

Haoxiang Guan, Jiyan He, Shuxin Zheng et al. · microsoft-research

Large language models (LLMs) have demonstrated impressive performance on many tasks. However, to achieve optimal performance, specially designed prompting methods are still needed. These methods either rely on task-specific few-shot examples that require a certain level of domain knowledge, or are designed to be simple but only perform well on a few types of tasks. In this work, we attempt to introduce the concept of generalist prompting, which operates on the design principle of achieving optimal or near-optimal performance on a wide range of tasks while eliminating the need for manual selection and customization of prompts tailored to specific problems. Furthermore, we propose MeMo (Mental Models), an innovative prompting method that is simple-designed yet effectively fulfills the criteria of generalist prompting. MeMo distills the cores of various prompting methods into individual mental models and allows LLMs to autonomously select the most suitable mental models for the problem, achieving or being near to the state-of-the-art results on diverse tasks such as STEM, logical reasoning, and commonsense reasoning in zero-shot settings. We hope that the insights presented herein will stimulate further exploration of generalist prompting methods for LLMs.